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- PDB-1ne6: Crystal structure of Sp-cAMP binding R1a subunit of cAMP-dependen... -

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Basic information

Entry
Database: PDB / ID: 1ne6
TitleCrystal structure of Sp-cAMP binding R1a subunit of cAMP-dependent protein kinase
ComponentscAMP-dependent protein kinase type I-alpha regulatory chain
KeywordsHYDROLASE / cAMP-dependent protein kinase / R1a subunit / cAMP analog / Sp-cAMP
Function / homology
Function and homology information


PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation ...PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation / cAMP-dependent protein kinase complex / sarcomere organization / Vasopressin regulates renal water homeostasis via Aquaporins / plasma membrane raft / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / immunological synapse / cAMP binding / cellular response to glucagon stimulus / multivesicular body / regulation of protein phosphorylation / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein domain specific binding / negative regulation of gene expression / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-SP1 / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, J. / Jones, J.M. / Xuong, N.H. / Taylor, S.S.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structures of RIalpha Subunit of Cyclic Adenosine 5'-Monophosphate (cAMP)-Dependent Protein Kinase Complexed with (R(p))-Adenosine 3',5'-Cyclic Monophosphothioate and (S(p))-Adenosine ...Title: Crystal Structures of RIalpha Subunit of Cyclic Adenosine 5'-Monophosphate (cAMP)-Dependent Protein Kinase Complexed with (R(p))-Adenosine 3',5'-Cyclic Monophosphothioate and (S(p))-Adenosine 3',5'-Cyclic Monophosphothioate, the Phosphothioate Analogues of cAMP.
Authors: Wu, J. / Jones, J.M. / Xuong, N.H. / Eyck, L.F. / Taylor, S.S.
History
DepositionDec 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase type I-alpha regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5713
Polymers31,8801
Non-polymers6912
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.4, 87.4, 178.7
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein cAMP-dependent protein kinase type I-alpha regulatory chain


Mass: 31880.104 Da / Num. of mol.: 1 / Fragment: 1-91 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKAR1A / Production host: Escherichia coli (E. coli) / References: UniProt: P00514
#2: Chemical ChemComp-SP1 / 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL / SP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE


Mass: 345.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O5PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: amino sulfate, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K
Crystal grow
*PLUS
Temperature: 22.5 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
21.0 M1reservoirNH2SO4
312.5 %glycerol1reservoir
410 mMdithiothreitol1reservoir
50.1 M1reservoirNaAcpH5.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 18621 / Num. obs: 17939 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 35.4 Å2 / Rsym value: 0.045 / Net I/σ(I): 63.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 6.6 / Num. unique all: 1585 / Rsym value: 0.451 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. obs: 18563 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.451

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RGS

1rgs


Resolution: 2.3→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 821 -random
Rwork0.211 ---
all-18621 --
obs-17939 99.5 %-
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.46 Å2-2.77 Å20 Å2
2---9.46 Å20 Å2
3---18.91 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 44 102 2243
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.43
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.04
RfactorNum. reflection% reflection
Rfree0.304 55 -
Rwork0.294 --
obs-1585 97.9 %
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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